Part I of the publication series addressed the fundamentals of lifetime assessment of prototype Francis turbines. This paper (Part II) focuses on the numerical part of the procedure. The essential steps and requirements shall be presented (background). The starting points for the numerical considerations are the pressure fields of the transient CFD simulations, which are exported per time step and applied to the existing structure via a fluid–structure interaction. That enables a transient mechanical stress calculation to be conducted, resulting in the fatigue analysis of the component to estimate the remaining lifetime. The individual model requirements should be represented accordingly and applied to the prototype facility (method). The results obtained from this application should be discussed and evaluated. It has to be mentioned that the validation of the numerical results will be performed at Part IV of this publication series (results). The present paper will end up discussing the results and conclusions about further data processing (Conclusion).